diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
index b73ca486c10a5a66ffd9ba052bfec3db81bc78f5..738ee3c13347c2a6a6d9d2e223340eb4ca3c21b0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
@@ -723,6 +723,7 @@ public class DatasetLister extends AbstractLister implements IDatasetLister
dataSet.setProductionDate(record.production_timestamp);
dataSet.setRegistrationDate(record.registration_timestamp);
dataSet.setRegistrator(getOrCreateRegistrator(record.pers_id_registerer));
+ dataSet.setModificationDate(record.modification_timestamp);
dataSet.setDataSetProperties(new ArrayList<IEntityProperty>());
if (record.ctnr_id != null)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetRecord.java
index 7477f825affc64212812dc215008b62ceb70d618..542fa8937811c087b55d19452d83e2d2cb62d7ab 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetRecord.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetRecord.java
@@ -27,6 +27,8 @@ public class DatasetRecord extends CodeRecord
public Date registration_timestamp;
+ public Date modification_timestamp;
+
public Long pers_id_registerer;
public boolean is_placeholder;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/DataSetBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/DataSetBuilder.java
index 14ed412a2c3bd2a5b415640518f186cc5f3a28d5..195caac5945a6824e6281ff28fe6423b14984543 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/DataSetBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/DataSetBuilder.java
@@ -27,6 +27,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStore;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
@@ -93,6 +94,12 @@ public class DataSetBuilder
return this;
}
+ public DataSetBuilder fileFormat(String fileFormatType)
+ {
+ dataSet.setFileFormatType(new FileFormatType(fileFormatType));
+ return this;
+ }
+
public DataSetBuilder status(DataSetArchivingStatus status)
{
dataSet.setStatus(status);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResults.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResults.java
index 95564639f7965361844615f46b2babb39316386b..b68ab4c4b2bcf5cc7fd9d9840260d7ceafde9cc5 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResults.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResults.java
@@ -100,31 +100,46 @@ public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoEx
DataSetInformation info = new DataSetInformation();
info.setExperimentIdentifier(experimentIdentifier);
String parentDataSetCodesOrNull = getProperty(properties, PARENT_DATA_SET_CODES);
+ String baseExperimentIdentifier = getProperty(properties, EXPERIMENT_IDENTIFIER_KEY);
+ List<String> parentDataSetCodes =
+ getParentDataSetCodes(parentDataSetCodesOrNull, baseExperimentIdentifier, service);
+ info.setParentDataSetCodes(parentDataSetCodes);
+ return info;
+ }
+
+ /**
+ * Returns data set codes either from the first argument or if <code>null</code> from
+ * the data sets of the specified experiment.
+ */
+ static List<String> getParentDataSetCodes(String parentDataSetCodesOrNull,
+ String baseExperimentIdentifier, IEncapsulatedOpenBISService service)
+ {
+ List<String> parentDataSetCodes = new ArrayList<String>();
if (parentDataSetCodesOrNull != null)
{
- info.setParentDataSetCodes(Arrays.asList(StringUtils.split(parentDataSetCodesOrNull, ", ")));
- } else
+ parentDataSetCodes = Arrays.asList(StringUtils.split(parentDataSetCodesOrNull, ", "));
+ } else
{
- String baseExperimentIdentifier = getProperty(properties, EXPERIMENT_IDENTIFIER_KEY);
if (baseExperimentIdentifier != null)
{
- ExperimentIdentifier identifier = new ExperimentIdentifierFactory(baseExperimentIdentifier).createIdentifier();
+ ExperimentIdentifier identifier =
+ new ExperimentIdentifierFactory(baseExperimentIdentifier)
+ .createIdentifier();
Experiment baseExperiment = service.tryToGetExperiment(identifier);
if (baseExperiment == null)
{
throw new UserFailureException("Property " + EXPERIMENT_IDENTIFIER_KEY
+ " specifies an unknown experiment: " + baseExperimentIdentifier);
}
- List<ExternalData> dataSets = service.listDataSetsByExperimentID(baseExperiment.getId());
- List<String> parentDataSetCodes = new ArrayList<String>();
+ List<ExternalData> dataSets =
+ service.listDataSetsByExperimentID(baseExperiment.getId());
for (ExternalData dataSet : dataSets)
{
parentDataSetCodes.add(dataSet.getCode());
}
- info.setParentDataSetCodes(parentDataSetCodes);
}
}
- return info;
+ return parentDataSetCodes;
}
private String getProperty(Properties properties, String key)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTask.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTask.java
new file mode 100644
index 0000000000000000000000000000000000000000..1c33685a0764e097481af8644dc520708811acb7
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTask.java
@@ -0,0 +1,175 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.regex.Pattern;
+
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.maintenance.IMaintenanceTask;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
+import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class ProteinResultDataSetParentLinkingTask implements IMaintenanceTask
+{
+ private static final Pattern DATA_SET_CODE_PATTERN = Pattern.compile("\\d{17}-\\d+");
+
+ private static final String PARENT_DATA_SET_CODES_KEY =
+ DataSetInfoExtractorForProteinResults.PARENT_DATA_SET_CODES.toUpperCase();
+
+ private static final String BASE_EXPERIMENT_KEY =
+ DataSetInfoExtractorForProteinResults.EXPERIMENT_IDENTIFIER_KEY.toUpperCase();
+
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ ProteinResultDataSetParentLinkingTask.class);
+
+ private final IEncapsulatedOpenBISService service;
+
+ public ProteinResultDataSetParentLinkingTask()
+ {
+ this(ServiceProvider.getOpenBISService());
+ }
+
+ ProteinResultDataSetParentLinkingTask(IEncapsulatedOpenBISService service)
+ {
+ this.service = service;
+
+ }
+
+ public void setUp(String pluginName, Properties properties)
+ {
+ }
+
+ public void execute()
+ {
+ List<DataSetUpdatesDTO> dataSetUpdates = new ArrayList<DataSetUpdatesDTO>();
+ List<Project> projects = service.listProjects();
+ for (Project project : projects)
+ {
+ List<Experiment> experiments =
+ service.listExperiments(new ProjectIdentifier(project.getSpace().getCode(),
+ project.getCode()));
+ for (Experiment experiment : experiments)
+ {
+ Map<String, IEntityProperty> propertiesMap = getPropertiesMap(experiment);
+ String baseExperimentIdentifier =
+ tryGetProperty(propertiesMap, BASE_EXPERIMENT_KEY);
+ String parentDataSetCodes =
+ tryGetProperty(propertiesMap, PARENT_DATA_SET_CODES_KEY);
+ List<String> codes =
+ filter(DataSetInfoExtractorForProteinResults.getParentDataSetCodes(
+ parentDataSetCodes, baseExperimentIdentifier, service));
+ if (codes.isEmpty())
+ {
+ continue;
+ }
+ List<ExternalData> dataSets =
+ service.listDataSetsByExperimentID(experiment.getId());
+ if (dataSets.isEmpty())
+ {
+ continue;
+ }
+ for (ExternalData ds : dataSets)
+ {
+ if (ds instanceof DataSet == false)
+ {
+ continue;
+ }
+ DataSet dataSet = (DataSet) ds;
+ DataSetUpdatesDTO update = new DataSetUpdatesDTO();
+ update.setDatasetId(new TechId(dataSet.getId()));
+ update.setVersion(dataSet.getModificationDate());
+ update.setExperimentIdentifierOrNull(ExperimentIdentifierFactory.parse(dataSet
+ .getExperiment().getIdentifier()));
+ update.setModifiedParentDatasetCodesOrNull(codes.toArray(new String[0]));
+ update.setFileFormatTypeCode(dataSet.getFileFormatType().getCode());
+ update.setProperties(dataSet.getProperties());
+ operationLog.info("Parent data set links of data set " + dataSet.getCode()
+ + " from experiment " + experiment.getIdentifier()
+ + " will be updated.");
+ dataSetUpdates.add(update);
+ }
+ }
+ }
+ service.performEntityOperations(new AtomicEntityOperationDetails(null, Collections
+ .<NewSpace> emptyList(), Collections.<NewProject> emptyList(), Collections
+ .<NewExperiment> emptyList(), Collections.<SampleUpdatesDTO> emptyList(),
+ Collections.<NewSample> emptyList(), Collections
+ .<String, List<NewMaterial>> emptyMap(), Collections
+ .<NewExternalData> emptyList(), dataSetUpdates));
+ operationLog.info("Parent data set links for " + dataSetUpdates.size()
+ + " data sets have been updated.");
+ }
+
+ private Map<String, IEntityProperty> getPropertiesMap(Experiment experiment)
+ {
+ List<IEntityProperty> properties = experiment.getProperties();
+ Map<String, IEntityProperty> propertiesMap = new HashMap<String, IEntityProperty>();
+ for (IEntityProperty property : properties)
+ {
+ propertiesMap.put(property.getPropertyType().getCode(), property);
+ }
+ return propertiesMap;
+ }
+
+ private String tryGetProperty(Map<String, IEntityProperty> propertiesMap, String key)
+ {
+ IEntityProperty property = propertiesMap.get(key);
+ return property == null ? null : property.tryGetAsString();
+ }
+
+ private List<String> filter(List<String> codes)
+ {
+ List<String> result = new ArrayList<String>();
+ for (String code : codes)
+ {
+ if (DATA_SET_CODE_PATTERN.matcher(code).matches())
+ {
+ result.add(code);
+ }
+ }
+ return result;
+ }
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTaskTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTaskTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..53aff1de1eb68aff9b0a59ba0a9cfec9c4b2343c
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTaskTest.java
@@ -0,0 +1,174 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
+
+import java.util.Arrays;
+import java.util.Date;
+import java.util.List;
+
+import org.apache.log4j.Level;
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.logging.BufferedAppender;
+import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class ProteinResultDataSetParentLinkingTaskTest extends AssertJUnit
+{
+ private static final String PARENT_DATA_SET_CODES_KEY =
+ DataSetInfoExtractorForProteinResults.PARENT_DATA_SET_CODES.toUpperCase();
+
+ private static final String BASE_EXPERIMENT_KEY =
+ DataSetInfoExtractorForProteinResults.EXPERIMENT_IDENTIFIER_KEY.toUpperCase();
+
+ private BufferedAppender logRecorder;
+
+ private Mockery context;
+
+ private IEncapsulatedOpenBISService service;
+
+ private ProteinResultDataSetParentLinkingTask task;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ logRecorder = new BufferedAppender("%-5p %c - %m%n", Level.DEBUG);
+ context = new Mockery();
+ service = context.mock(IEncapsulatedOpenBISService.class);
+ task = new ProteinResultDataSetParentLinkingTask(service);
+ }
+
+ @AfterMethod
+ public void afterMethod()
+ {
+ logRecorder.reset();
+ // To following line of code should also be called at the end of each test method.
+ // Otherwise one do not known which test failed.
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void test()
+ {
+ final Experiment e1 =
+ new ExperimentBuilder().id(1).identifier("/S/P1/E1").property("ABC", "non-sense")
+ .getExperiment();
+ final Experiment e2 =
+ new ExperimentBuilder().id(2).identifier("/A/P2/E2")
+ .property(PARENT_DATA_SET_CODES_KEY, "non-sense").getExperiment();
+ final Experiment e3 =
+ new ExperimentBuilder()
+ .id(3)
+ .identifier("/A/P2/E3")
+ .property(PARENT_DATA_SET_CODES_KEY,
+ "20100930111833087-297733, 20100511163311581-25265")
+ .getExperiment();
+ final Experiment e4 =
+ new ExperimentBuilder().id(4).identifier("/S/P1/E4")
+ .property(BASE_EXPERIMENT_KEY, "/S/P1/E1").getExperiment();
+ final DataSet ds1 =
+ new DataSetBuilder(1).code("20100930111811581-25265").fileFormat("A")
+ .experiment(e1).modificationDate(new Date(11)).getDataSet();
+ final DataSet ds2 =
+ new DataSetBuilder(2).code("20100930111811087-29765").fileFormat("B")
+ .experiment(e4).modificationDate(new Date(22)).getDataSet();
+ final DataSet ds3 =
+ new DataSetBuilder(3).code("20100530111833087-297733").fileFormat("C")
+ .experiment(e3).modificationDate(new Date(33)).property("ALPHA", "3.1")
+ .getDataSet();
+ final RecordingMatcher<AtomicEntityOperationDetails> operationRecorder =
+ new RecordingMatcher<AtomicEntityOperationDetails>();
+ context.checking(new Expectations()
+ {
+ {
+ one(service).listProjects();
+ will(returnValue(Arrays.asList(e1.getProject(), e2.getProject())));
+
+ one(service).listExperiments(new ProjectIdentifier("S", "P1"));
+ will(returnValue(Arrays.asList(e1, e4)));
+
+ one(service).listExperiments(new ProjectIdentifier("A", "P2"));
+ will(returnValue(Arrays.asList(e2, e3)));
+
+ one(service).tryToGetExperiment(ExperimentIdentifierFactory.parse("/S/P1/E1"));
+ will(returnValue(e1));
+
+ one(service).listDataSetsByExperimentID(e1.getId());
+ will(returnValue(Arrays.asList(ds1)));
+
+ one(service).listDataSetsByExperimentID(e3.getId());
+ will(returnValue(Arrays.asList(ds3)));
+
+ one(service).listDataSetsByExperimentID(e4.getId());
+ will(returnValue(Arrays.asList(ds2)));
+
+ one(service).performEntityOperations(with(operationRecorder));
+ }
+ });
+
+ task.execute();
+
+ assertEquals("INFO OPERATION.ProteinResultDataSetParentLinkingTask - "
+ + "Parent data set links of data set 20100930111811087-29765 "
+ + "from experiment /S/P1/E4 will be updated.\n"
+ + "INFO OPERATION.ProteinResultDataSetParentLinkingTask - "
+ + "Parent data set links of data set 20100530111833087-297733 "
+ + "from experiment /A/P2/E3 will be updated.\n"
+ + "INFO OPERATION.ProteinResultDataSetParentLinkingTask - "
+ + "Parent data set links for 2 data sets have been updated.",
+ logRecorder.getLogContent());
+ List<DataSetUpdatesDTO> dataSetUpdates =
+ operationRecorder.recordedObject().getDataSetUpdates();
+ assertEquals(2L, dataSetUpdates.get(0).getDatasetId().getId().longValue());
+ assertEquals(22L, dataSetUpdates.get(0).getVersion().getTime());
+ assertEquals("B", dataSetUpdates.get(0).getFileFormatTypeCode());
+ assertEquals("[]", dataSetUpdates.get(0).getProperties().toString());
+ assertEquals(e4.getIdentifier(), dataSetUpdates.get(0).getExperimentIdentifierOrNull()
+ .toString());
+ assertEquals("[20100930111811581-25265]",
+ Arrays.asList(dataSetUpdates.get(0).getModifiedParentDatasetCodesOrNull())
+ .toString());
+ assertEquals(3L, dataSetUpdates.get(1).getDatasetId().getId().longValue());
+ assertEquals(33L, dataSetUpdates.get(1).getVersion().getTime());
+ assertEquals("C", dataSetUpdates.get(1).getFileFormatTypeCode());
+ assertEquals("[ALPHA: 3.1]", dataSetUpdates.get(1).getProperties().toString());
+ assertEquals(e3.getIdentifier(), dataSetUpdates.get(1).getExperimentIdentifierOrNull()
+ .toString());
+ assertEquals("[20100930111833087-297733, 20100511163311581-25265]",
+ Arrays.asList(dataSetUpdates.get(1).getModifiedParentDatasetCodesOrNull())
+ .toString());
+ assertEquals(2, dataSetUpdates.size());
+ context.assertIsSatisfied();
+ }
+
+}